The man is believed to have sustained a broken leg in the crash, which happened about 10:25am.
The incident took place near the Scotland’s Charity Air Ambulance (SCAAA) headquarters.
Officials confirmed the pilot had been taken to hospital.
He was the only person on board at the time of the crash.
Police Scotland will launch an investigation into the incident.
A spokesman said: “There is no danger to the public and an investigation will follow. The airport remains open.”
Eyewitnesses reported the helicopter being left a “mangled mess”.
Connor Wojtowicz, 23, who lives at the airport, was among the first on the scene.
“I was sitting in my room, which is 150ft from where the helicopter came down,” Mr Wojtowicz told the Courier.
“I heard it take off and it didn’t sound right at all – then there was a bang.”
A Police Scotland spokesperson said: “There is one male casualty with a leg injury.”
The helicopter is understood to be used for training purposes.
An image of the crash showed the aircraft lying on its side with the rotors and tail badly damaged.
It is not known if the helicopter crashed due to a failed take-off or a hard landing at the airfield at New Scone, which is used for private and business flights.